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(-) Description

Title :  STRUCTURE OF THE MG2+-BOUND SYNAPTOTAGMIN-1 SNARE COMPLEX (SHORT UNIT CELL FORM)
 
Authors :  Q. Zhou, M. Zhao, A. Y. Lyubimov, M. Uervirojnangkoorn, W. I. Weis, A. T.
Date :  02 Jul 15  (Deposition) - 12 Aug 15  (Release) - 16 Sep 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  4.10
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A (1x),B (1x),C (1x),D (1x),E (1x),F (2x)
Keywords :  Synaptic Fusion Complex, Synaptotagmin1, Neuronal Snare Complex, Endocytosis, Exocytosis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Q. Zhou, Y. Lai, T. Bacaj, M. Zhao, A. Y. Lyubimov, M. Uervirojnangkoorn, O. B. Zeldin, A. S. Brewster, N. K. Sauter, A. E. Cohen, S. M. Soltis, R. Alonso-Mori, M. Chollet, H. T. Lemke, R. A. Pfuetzner, U. B. Choi, W. I. Weis, J. Diao, T. C. Sudhof, A. T. Brunger
Architecture Of The Synaptotagmin-Snare Machinery For Neuronal Exocytosis.
Nature V. 525 62 2015
PubMed-ID: 26280336  |  Reference-DOI: 10.1038/NATURE14975

(-) Compounds

Molecule 1 - VESICLE-ASSOCIATED MEMBRANE PROTEIN 2
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PACYCDUET-1
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 28-89
    Gene: VAMP2, SYB2
    Organism Common: RAT
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116
    Synonym: VAMP-2,SYNAPTOBREVIN-2
 
Molecule 2 - SYNTAXIN-1A
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PACYCDUET-1
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 191-256
    Gene: STX1A, SAP
    Organism Common: RAT
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116
    Synonym: NEURON-SPECIFIC ANTIGEN HPC-1,SYNAPTOTAGMIN-ASSOCIATED 35 KDA PROTEIN,P35A
 
Molecule 3 - SYNAPTOSOMAL-ASSOCIATED PROTEIN 25
    Chains: C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PETDUET-1
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 7-83
    Gene: SNAP25, SNAP
    Organism Common: RAT
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116
    Synonym: SNAP-25,SUPER PROTEIN,SUP,SYNAPTOSOMAL-ASSOCIATED 25 KDA PROTEIN
 
Molecule 4 - SYNAPTOSOMAL-ASSOCIATED PROTEIN 25
    Chains: D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PETDUET-1
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 141-204
    Gene: SNAP25, SNAP
    Organism Common: RAT
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116
    Synonym: SNAP-25,SUPER PROTEIN,SUP,SYNAPTOSOMAL-ASSOCIATED 25 KDA PROTEIN
 
Molecule 5 - SYNAPTOTAGMIN-1
    Chains: E, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PETDUET-1
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 141-421
    Gene: SYT1
    Organism Common: RAT
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116
    Synonym: SYNAPTOTAGMIN I,SYTI,P65

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (2x): A (1x)B (1x)C (1x)D (1x)E (1x)F (2x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1MG4Ligand/IonMAGNESIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP E:303 , ASP E:309 , ASP E:363 , TYR E:364 , ASP E:365binding site for residue MG E 501
2AC2SOFTWAREASP E:172 , ASP E:178 , PHE E:231 , ASP E:232 , GLU E:346binding site for residue MG E 502
3AC3SOFTWAREASP F:172 , ASP F:178 , PHE F:231 , GLU F:346binding site for residue MG F 501
4AC4SOFTWAREMET F:302 , ASP F:363 , ASP F:365binding site for residue MG F 502
5AC5SOFTWARELEU F:185 , LEU F:186 , PRO F:187 , LYS F:189 , LYS F:191 , LYS F:192 , VAL F:214binding site for Di-peptide ASP F 188 and LYS F 190
6AC6SOFTWARELEU F:185 , LEU F:186 , PRO F:187 , LYS F:189 , LYS F:191 , LYS F:192 , VAL F:214binding site for Di-peptide ASP F 188 and LYS F 190

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5CCI)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5CCI)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5CCI)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5CCI)

(-) Exons   (0, 0)

(no "Exon" information available for 5CCI)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:62
                                                                                              
               SCOP domains -------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------- Transcript
                 5cci A  28 SNRRLQQTQAQVDEVVDIMRVNVDKVLERDQKLSELDDRADALQAGASQFETSAAKLKRKYW  89
                                    37        47        57        67        77        87  


Chain B from PDB  Type:PROTEIN  Length:67
                                                                                                   
               SCOP domains ------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------- Transcript
                 5cci B 190 MALSEIETRHSEIIKLENSIRELHDMFMDMAMLVESQGEMIDRIEYNVEHAVDYVERAVSDTKKAVK 256
                                   199       209       219       229       239       249       


Chain C from PDB  Type:PROTEIN  Length:73
                                                                                                         
               SCOP domains ------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------- Transcript
                 5cci C  10 ELEEMQRRADQLADESLESTRRMLQLVEESKDAGIRTLVMLDEQGEQLDRVEEGMNHINQDMKEAEKNLKDLG  82
                                    19        29        39        49        59        69        79   


Chain D from PDB  Type:PROTEIN  Length:64
                                                                                                
               SCOP domains ---------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------- Transcript
                 5cci D 140 MARENEMDENLEQVSGIIGNLRHMALDMGNEIDTQNRQIDRIMEKADSNKTRIDEANQRATKML 203
                                   149       159       169       179       189       199    


Chain E from PDB  Type:PROTEIN  Length:280
                                                                                                                                                                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeee....eeeeeeeeee............eeeeeee.......ee..........eeeeeeee..hhhhhh..eeeeeeee........eeeeeeee.........eeeeee.............eeeeeeeee....eeeeeeeeee............eeeeeeeee..eeeeeee..........eeeeeeeee....hhhh.eeeeeeee........eeeeeeee....hhhhhhhhhhhhh....eeeeee..hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5cci E 141 KLGKLQYSLDYDFQNNQLLVGIIQAAELPALDMGGTSDPYVKVFLLPDKKKKFETKVHRKTLNPVFNEQFTFKVPYSELGGKTLVMAVYDFDRFSKHDIIGEFKVPMNTVDFGHVTEEWRDLQSAEKEEQEKLGDICFSLRYVPTAGKLTVVILEAKNLKKMDVGGLSDPYVKIHLMQNGKRLKKKKTTIKKNTLNPYYNESFSFEVPFEQIQKVQVVVTVLDYDKIGKNDAIGKVFVGYNSTGAELRHWSDMLANPRRPIAQWHTLQVEEEVDAMLAVK 420
                                   150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420


Chain F from PDB  Type:PROTEIN  Length:268
                                                                                                                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeee....eeeeeeeeee............eeeeeee.......ee..........eeeeeeee..hhhhhh..eeeeeeee........eee..eee.........eeeeee.......eeeeeeeee....eeeeeeeeee.......eeeeeeeee..eeeeeee..........eeeeeeeee....hhhh.eeeeeeee.........eeeeee....hhhhhhhhhhhhh....eeeeee..hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5cci F 141 KLGKLQYSLDYDFQNNQLLVGIIQAAELPALDMGGTSDPYVKVFLLPDKKKKFETKVHRKTLNPVFNEQFTFKVPYSELGGKTLVMAVYDFDRFSKHDIIGEFKVPMNTVDFGHVTEEWRDLQSAEKGDICFSLRYVPTAGKLTVVILEAKNLKKMSDPYVKIHLMQNGKRLKKKKTTIKKNTLNPYYNESFSFEVPFEQIQKVQVVVTVLDYDKGKNDAIGKVFVGYNSTGAELRHWSDMLANPRRPIAQWHTLQVEEEVDAMLAVK 420
                                   150       160       170       180       190       200       210       220       230       240       250       260      |276       286       296     ||311       321       331       341       351       361    || 372       382       392       402       412        
                                                                                                                                                        267|                         302|                                                       366|                                                    
                                                                                                                                                         274                          308                                                        368
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 5CCI)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5CCI)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5CCI)

(-) Gene Ontology  (134, 212)

Asymmetric Unit(hide GO term definitions)

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  STX1A_RAT | P32851
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  SYT1_RAT | P21707
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  VAMP2_RAT | P63045
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        SNP25_RAT | P60881: 1jth 1n7s 1sfc 1uee 1urq 3hd7 3ipd 3j96 3j97 3j98 3j99 5ccg 5cch 5kj7 5kj8 5lob 5low
        STX1A_RAT | P32851: 1br0 1ez3 1hvv 1jth 1kil 1n7s 1sfc 1urq 2bu0 2m8r 2n1t 3c98 3hd7 3ipd 3j96 3j97 3j98 3j99 3rk2 3rk3 3rl0 4jeh 4jeu 5ccg 5cch 5kj7 5kj8
        SYT1_RAT | P21707: 1byn 1k5w 1rsy 1tjm 1tjx 1uov 1uow 2yoa 4wee 5ccg 5cch 5ccj 5kj7 5kj8
        VAMP2_RAT | P63045: 1kil 1n7s 1sfc 2bu0 2kog 2n1t 3hd7 3ipd 3j96 3j97 3j98 3j99 5ccg 5cch

(-) Related Entries Specified in the PDB File

5ccg 5cch